Variant report

Variant	rs7667469
Chromosome Location	chr4:80497692-80497693
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:79964140..79964963-chr4:80497048..80497852,2	MCF-7	breast:
2	chr4:80163067..80163617-chr4:80497361..80497863,2	MCF-7	breast:
3	chr4:80162158..80162658-chr4:80497305..80497853,2	MCF-7	breast:
4	chr4:79963311..79963867-chr4:80497354..80497886,2	MCF-7	breast:
5	chr4:79963329..79963907-chr4:80497328..80498247,2	K562	blood:

Extended variants
information (count: 88 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10004226	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10022309	0.84[ASN][1000 genomes]
rs10022314	0.84[ASN][1000 genomes]
rs10022663	0.99[ASN][1000 genomes]
rs10025630	0.84[ASN][1000 genomes]
rs10033410	0.84[ASN][1000 genomes]
rs1031004	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1031005	0.94[ASN][1000 genomes]
rs11098741	0.84[ASN][1000 genomes]
rs11098742	0.84[ASN][1000 genomes]
rs11098762	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11098764	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11098766	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11098770	0.94[ASN][1000 genomes]
rs11728755	0.92[ASN][1000 genomes]
rs11736369	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11941782	0.96[ASN][1000 genomes]
rs12500146	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12501981	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12502224	0.84[ASN][1000 genomes]
rs12507160	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12507375	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12510204	0.84[ASN][1000 genomes]
rs12510243	0.84[ASN][1000 genomes]
rs12511646	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12513177	0.84[ASN][1000 genomes]
rs12639996	0.84[ASN][1000 genomes]
rs12640638	0.84[ASN][1000 genomes]
rs12643491	0.94[ASN][1000 genomes]
rs12643976	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13104009	0.94[ASN][1000 genomes]
rs13112067	0.96[ASN][1000 genomes]
rs13112577	0.96[ASN][1000 genomes]
rs13124357	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13127970	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13128134	0.84[ASN][1000 genomes]
rs13129838	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13142610	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13144408	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13146986	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1348086	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1371989	0.94[ASN][1000 genomes]
rs1371993	0.96[ASN][1000 genomes]
rs1371996	0.83[ASN][1000 genomes]
rs1440852	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1440853	1.00[ASN][1000 genomes]
rs1440854	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1440864	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1440865	0.84[ASN][1000 genomes]
rs1440866	0.84[ASN][1000 genomes]
rs1595966	0.84[ASN][1000 genomes]
rs17003985	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1837645	0.96[ASN][1000 genomes]
rs1837646	0.96[ASN][1000 genomes]
rs1837647	0.86[ASN][1000 genomes]
rs1975399	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1992367	0.82[ASN][1000 genomes]
rs2119421	0.82[ASN][1000 genomes]
rs2165386	1.00[ASN][1000 genomes]
rs2165387	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2165388	0.84[ASN][1000 genomes]
rs2196978	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2867672	0.84[ASN][1000 genomes]
rs2903640	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35487709	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35631270	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3943669	0.94[ASN][1000 genomes]
rs4389603	0.99[ASN][1000 genomes]
rs4443312	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4975053	0.84[ASN][1000 genomes]
rs4975054	0.84[ASN][1000 genomes]
rs4975055	0.84[ASN][1000 genomes]
rs4975056	0.95[ASN][1000 genomes]
rs4975057	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4975097	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6812760	0.96[ASN][1000 genomes]
rs6850999	1.00[ASN][1000 genomes]
rs6852514	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71629061	0.85[ASN][1000 genomes]
rs7697359	0.84[ASN][1000 genomes]
rs9307545	0.94[ASN][1000 genomes]
rs9307551	0.94[ASN][1000 genomes]
rs968176	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999174	chr4:80212935-80512356	Enhancers Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv879506	chr4:80316417-80604625	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv879507	chr4:80365765-80552199	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv879508	chr4:80398708-80552199	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1002031	chr4:80459528-80759113	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7667469	LINC00989	cis	Muscle Skeletal	GTEx
rs7667469	LINC00989	cis	Skin Sun Exposed Lower leg	GTEx
rs7667469	LINC00989	cis	Adipose Subcutaneous	GTEx
rs7667469	LINC00989	cis	Whole Blood	GTEx

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:80495600-80497800	Enhancers	iPS-15b Cell Line	embryonic stem cell
2	chr4:80495600-80497800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr4:80495800-80497800	Enhancers	HUES6 Cell Line	embryonic stem cell
4	chr4:80495800-80497800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr4:80496000-80497800	Enhancers	Adipose Nuclei	Adipose
6	chr4:80496400-80497800	Enhancers	Fetal Heart	heart
7	chr4:80496600-80499800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr4:80497000-80497800	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr4:80497000-80497800	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr4:80497000-80497800	Enhancers	Pancreas	Pancrea
11	chr4:80497200-80497800	Enhancers	Colon Smooth Muscle	Colon
12	chr4:80497200-80497800	Enhancers	K562	blood
13	chr4:80497200-80498000	Enhancers	Duodenum Smooth Muscle	Duodenum
14	chr4:80497200-80498000	Enhancers	Stomach Smooth Muscle	stomach
15	chr4:80497400-80497800	Enhancers	Fetal Brain Male	brain
16	chr4:80497600-80497800	Enhancers	Ovary	ovary
17	chr4:80497600-80506200	Weak transcription	Placenta	Placenta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links